Multiplexed In Vivo Screening Using Barcoded Aptamer Technology to Identify Oligonucleotide-Based Targeting Reagents

Area of Science:

• Biotechnology
• Oligonucleotide Therapeutics
• Molecular Diagnostics

Background:

• Oligonucleotides, including mRNA vaccines and antisense oligonucleotides, are increasingly successful therapeutics.
• Aptamers show promise as affinity reagents for targeting biomarkers, but clinical translation is hindered by formulation challenges.
• Optimizing aptamer biostability and biodistribution for in vivo use requires extensive, time-consuming postselection manipulation.

Purpose of the Study:

• To introduce barcoded aptamer technology (BApT) for multiplexed screening of aptamer formulations.
• To overcome the bottleneck in identifying clinically useful aptamer reagents with improved pharmacokinetic properties.
• To simultaneously evaluate multiple aptamer formulations for targeting Non-Small Cell Lung Cancer (NSCLC) in vitro and in vivo.

Main Methods:

• Development and application of barcoded aptamer technology (BApT) for simultaneous screening.
• Investigation of 20 distinct aptamer formulations with varying molecular designs.
• In vitro and in vivo assessment of aptamer targeting efficiency and biodistribution in NSCLC models.

Main Results:

• In vitro screening identified a 45 kDa bispecific aptamer formulation as optimal for cancer cell targeting.
• In vivo screening revealed a 30 kDa monomeric aptamer formulation as the best for tumor-specific targeting.
• The BApT pipeline identified shared biodistribution patterns among aptamer formulations with similar molecular architectures.

Conclusions:

• Barcoded aptamer technology (BApT) provides a powerful platform for multiplexed screening of aptamer formulations.
• This approach significantly accelerates the identification of optimized aptamers for therapeutic and diagnostic applications.
• BApT has broad potential for advancing fields requiring oligonucleotide-based targeting reagents.